macOS
Homebrewverifiziert · 100%
brew install jellyfishlocal Homebrew formula metadata
brew
jellyfish mit Homebrew, apt, Nix installieren
Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für jellyfish in AI-Agent-Workflows.
Installation
Weitere Installationsbefehle
Linux
Debian aptverifiziert · 92%
sudo apt install jellyfishDebian stable package indexes · jellyfish · Quelle: deb.debian.org
Nixverifiziert · 92%
nix profile install nixpkgs#jellyfishnixpkgs package indexes · pkgs/by-name/je/jellyfish/package.nix · Quelle: api.github.com
Überblick
Paketzusammenfassung
Fast, memory-efficient counting of DNA k-mers
Projektlinks
Befehle und Aliase
- jellyfish
Verlauf
Projektgeschichte und Nutzung
Jellyfish is a fast, memory-efficient k-mer counter for DNA sequence data. The project README and University of Maryland page describe it as a command-line tool that counts k-mers with a compact hash table and compare-and-swap-based parallelism.
Projektgeschichte
Jellyfish originated with Guillaume Marcais and Carl Kingsford's 2011 Bioinformatics paper, which proposed both a new k-mer counting algorithm and its implementation. The README asks researchers to cite that paper and summarizes the design as an order-of-magnitude memory and speed improvement over other k-mer counters.
The University of Maryland project page preserves the version-1 line and notes that Jellyfish 2.0 moved to a new location with enhancements such as support for longer k-mer sizes and better dynamic memory management. The GitHub repository later became the source and release hub for the 2.x codebase.
Adoptionsgeschichte
Jellyfish became a standard packaged bioinformatics utility because k-mer counting is a common preprocessing step in genome assembly, error correction, and sequence analysis. The README documents installation through Debian and Ubuntu apt, Arch AUR, FreeBSD ports, Cygwin or WSL workflows on Windows, and source builds; the batch input also records Homebrew, Debian, Nix, and Ubuntu packages.
Wie es verwendet wird
Typical use runs jellyfish count on FASTA or multi-FASTA input, then uses commands such as dump, stats, histo, merge, and query to inspect or combine the binary count database. The README also documents C++, Python, Ruby, and Perl bindings for reading Jellyfish output in scripts.
Warum Paket-Nerds sich dafür interessieren
For package nerds, Jellyfish is significant because it is not merely a helper binary; it packages a cited algorithm as a reusable command-line primitive for bioinformatics pipelines. Its presence in general-purpose package managers makes a research-grade k-mer counter available without each workflow vendoring its own build.
Zeitleiste
- 2011: Bioinformatics paper was first published online on January 7.
- 2011: University of Maryland page documented Jellyfish as a fast, parallel k-mer counter for DNA.
- 2012: Preserved manuals for the 1.1 series document the classic count, merge, dump, stats, histo, and query workflow.
- Version 2.0: University of Maryland page notes longer k-mer support and better dynamic memory management.
- 2.x: GitHub repository became the source, release, documentation, and bindings hub.
Related projects
- Related projects include other k-mer counters and genome-analysis tools, plus Quake-era workflows referenced by the older manual commands qhisto, qdump, and qmerge. The repository also relates to scripting-language bindings through SWIG.
Quellen
- https://academic.oup.com/bioinformatics/article/27/6/764/234905
- https://formulae.brew.sh/formula/jellyfish
- https://github.com/gmarcais/Jellyfish
- https://github.com/gmarcais/Jellyfish#readme
- https://github.com/gmarcais/Jellyfish/tree/master/doc
- https://pubmed.ncbi.nlm.nih.gov/21217122/
- https://www.cbcb.umd.edu/software/jellyfish/index.shtml
Sicherheitslage
Risikostufe: grün
narrow executable package without higher-risk signals.
Risikoklassifikator
grün Risiko · niedrig Konfidenz · appliance
Warum
- narrow executable package without higher-risk signals
Signale
- metadata:no-higher-risk-signals
Installationsverhalten
- In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
- Homebrew-Bottle-Metadaten sind für 10 Plattformziele verfügbar.
- Installiert mit 1 Laufzeitabhängigkeiten.
- Build-Metadaten listen 1 Build-Abhängigkeiten.
Empfohlene Prüfung
Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.
Executables
Installierte Executables
| Befehl | Art | Sichtbarkeit | Hinweis |
|---|---|---|---|
jellyfish | cli | globales Executable |
Aktualität
Version und Aktualität
Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.
Seite generiert2026-07-10
Manager-Version2.3.1
Manager aktualisiert2026-06-19
lokale DatenOK
Upstreamnot checked
neueste erkannte Versionnicht erkannt
https://github.com/gmarcais/Jellyfish
- InfoNo cached GitHub release or tag data was available.https://github.com/gmarcais/Jellyfishnone Konfidenz
Installationsmetadaten
Paketmetadaten
| Paketschlüssel | brew:jellyfish |
|---|---|
| Version | 2.3.1 |
| Paketmanager | Homebrew |
| Paketmanager-Seite | https://formulae.brew.sh/formula/jellyfish |
| Homepage | https://github.com/gmarcais/Jellyfish |
| Repository | https://github.com/gmarcais/Jellyfish |
| Upstream-Dokumentation | https://github.com/gmarcais/Jellyfish#readme |
| Lizenz | BSD-3-Clause OR GPL-3.0-or-later |
| Quellarchiv | https://github.com/gmarcais/Jellyfish/releases/download/v2.3.1/jellyfish-2.3.1.tar.gz |
| Zuletzt aktualisiert | 2026-06-19T12:31:21-07:00 |
| Pulse | updated |
| Abhängigkeiten | htslib |
| Build-Abhängigkeiten | pkgconf |
| Bottle | verfügbar (auf arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, monterey, sonoma, ventura, x86_64_linux) |
| Homebrew post-install | nicht definiert |
| Dienst | keiner deklariert |
Registry-Fakten
Details aus der Quelldatenbank
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | jellyfish |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
Source-Datenbank-Treffer
Andere Paketmanager-Einträge
Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.
Debian apt95%
jellyfish 2.3.1-4+b1
count k-mers in DNA sequences
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish- Section: science
- Architecture: amd64
- Source Package: jellyfish
- 5 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Debian apt95%
jellyfish-examples 2.3.1-4
count k-mers in DNA sequences (examples for testing)
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish-examples- Section: science
- Architecture: all
- Source Package: jellyfish
- 1 optionale Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Debian apt95%
libjellyfish-2.0-2 2.3.1-4+b1
count k-mers in DNA sequences (dynamic library of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-2- Section: libs
- Architecture: amd64
- Source Package: jellyfish
- 3 Abhängigkeiten
- 1 stellt bereit
- normalized package name match
- Abgeglichen nach: Jellyfish
Debian apt95%
libjellyfish-2.0-dev 2.3.1-4+b1
count k-mers in DNA sequences (development files of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-dev- Section: libdevel
- Architecture: amd64
- Source Package: jellyfish
- 1 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Debian apt95%
libjellyfish-perl 2.3.1-4+b1
count k-mers in DNA sequences (Perl bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-perl- Section: perl
- Architecture: amd64
- Source Package: jellyfish
- 4 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Debian apt95%
python3-dna-jellyfish 2.3.1-4+b1
count k-mers in DNA sequences (Python bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install python3-dna-jellyfish- Section: python
- Architecture: amd64
- Source Package: jellyfish
- 5 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Nix95%
jellyfish
nix profile install nixpkgs#jellyfish- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
jellyfish 2.3.1-3build1
count k-mers in DNA sequences
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish- Section: universe/science
- Architecture: amd64
- 5 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
jellyfish-examples 2.3.1-3build1
count k-mers in DNA sequences (examples for testing)
https://www.genome.umd.edu/jellyfish.html
sudo apt install jellyfish-examples- Section: universe/science
- Architecture: all
- Source Package: jellyfish
- 1 optionale Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
libjellyfish-2.0-2 2.3.1-3build1
count k-mers in DNA sequences (dynamic library of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-2- Section: universe/libs
- Architecture: amd64
- Source Package: jellyfish
- 3 Abhängigkeiten
- 1 stellt bereit
- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
libjellyfish-2.0-dev 2.3.1-3build1
count k-mers in DNA sequences (development files of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-2.0-dev- Section: universe/libdevel
- Architecture: amd64
- Source Package: jellyfish
- 1 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
libjellyfish-perl 2.3.1-3build1
count k-mers in DNA sequences (Perl bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install libjellyfish-perl- Section: universe/perl
- Architecture: amd64
- Source Package: jellyfish
- 4 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Ubuntu apt95%
python3-dna-jellyfish 2.3.1-3build1
count k-mers in DNA sequences (Python bindings of jellyfish)
https://www.genome.umd.edu/jellyfish.html
sudo apt install python3-dna-jellyfish- Section: universe/python
- Architecture: amd64
- Source Package: jellyfish
- 5 Abhängigkeiten
- normalized package name match
- Abgeglichen nach: Jellyfish
Quellspur
Aus Repository-Daten generiert
Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.
Combined YAML source
View the package source record on GitHub.
Verwendete Quellen
- Geiger risk classifier
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment